D.C. Mayor Walter E. Washington formally recommended yesterday a residential real estate tax rate of $1.54 for each $100 of assessed value, a figure 3 cents less than previously estimated.

If adopted by the City Council, the lowered figure would shave another $12.30 off the taxes due from the owner-occupant of a $50,000 home.

Under existing tax laws and this year's $1.83 rate, the owner of such a home would owe $765.20. Under the previously estimated $1.57 rate, he would owe $643.70. The new proposed rate would cut that to $631.40.

The mayor recommended a commerical tax rate of $1.83 per $100 of valuation, the same rate as is now charged on all real estate in the city.

The new rates would apply to tax bills to be sent out in August, with the first installment payable in September and the balance next March.

Earlier this week, the City Council voted preliminary approval to a tax law permitting the two-level taxation, with the residential rate lower than the commercial. Final approval is expected July 11.

The two-level tax feature was proposed, independetly of each other, by the mayor and by Marion Barry (D-At Large), chairman of the council's committee on finance and revenue and a rival mayoral candidate.

In a related development yesterday, R. Robert Linowes, president of the Metropolitan Washington Board of Trade, accused the backers of the two-level tax of "political motivation." He predicted the new system would complicate tax administration while discouraging business growth in the city.

By law, the mayor must submit his recommended tax rate to the council by July 1. He reported total assessments in the city of $9.1 billion, of which $5.8 billion is residential (including apartment houses) and $3.3 billion is commercial.

The mayor said the additional 3-cent reduction in the residential rate became possible because fewer homeowners filed tax exemption affidavits than had been expected. When those forms were mailed out by the city last winter, there were reports that many homeowners tossed them out, not realizing their purpose.

Those who filed the affidavits will qualify for a homeowner's exemption. Under existing law, the first $6,000 of an owner-occupied home is exempt from taxation. Under the measure now making its way through the council, the exemption would rise to $9,000.

The mayor estimated that the average homeowner's tax would drop $169 under the new rate. Even with a 24 percent cut in the residential tax rate, the mayor said the city's total real estate tax yield from higher valuations should rise from $156 million last year to $163.8 million in the current fiscal year.

In his letter to the council, the mayor urged passage of his own measure rather than the one sponsored by Barry. The two differ mainly in the credits homeowners can claim on their city income taxes.